The regulatory role of HOX interacting lncRNA in oral cancer—An in silico analysis

Abstract

Objectives: We aim to elucidate the interaction of long noncoding RNAs with HOX genes and their regulatory role and potential drug candidates in oral cancer. Materials and Methods:The interaction network was constructed using RNA Interactome and the RNA Interactome from the Sequencing Experiments database. The differential expression of HOX genes and HOX interacting lncRNAs was assessed using the TCGA-Head and Neck Squamous Cell Carcinoma oral cancer dataset using DESeq2 R-package. Further, the functional enrichment analysis was performed for the differentially expressed HOX genes and HOX-interacting lncRNAs using Gene Ontology, long noncoding RNA Set Enrichment Analysis, lncRNA ontology annotation extractor and repository (Lantern), and LncRNA Ontology tools. Drug-lncRNA interaction and the effect of drugs on lncRNA expression were assessed from the D-lnc tool.Results: A total of 78 unique interactions were identified between HOX and lncRNAs.

The Mission of Long Non-Coding RNAs in Human Adult Renal Stem/Progenitor Cells and Renal Diseases

“…Recent studies devised a “chromatin-RNA reverse transcription in situ sequencing” (CRIST-seq) approach to profile the lncRNA interaction network in gene regulatory elements, uncovering a true lncRNA interaction network specific for the pluripotency in the Sox2 and Pou5f1 promoters [ 36 ]. The regulatory role of differentially expressed HOX-interacting lncRNAs in various biological processes and cancer hallmark events has been demonstrated by building interaction networks of lncRNA [ 37 ].…”